From a religious viewpoint, I believe that many theists would would say that their god is perfect and the standard of morality to which everything is compared. Should something waver from this standard, it is immoral. A theist that believes in an unchanging god might then reason that a non theist, or a thiest that believes in a god that changes or is not eternal in its attributes, is not capable of operating under a seperate moral code because their code would be subject to change as they or their god changes. One is capable of acting morally if their actions fall under the fixed code, but their actions would not be moral because of their own seperate code, but because they coincide with the higher code.
Looking back to the example given from 1 Samuel, a Christian would likely reason that the actions of the Hebrew army were moral because punishment of “evil”, as defined by their god, is a moral action. Things are very rarely black and white. While most would say that killing, for example, is not good, it can be justified and moral should the conditions satisfy the proper conditions.